FPGA implementation of a data-driven stochastic biochemical simulator with the next reaction method

Masato Yoshimi, Yow Iwaoka, Yuri Nishikawa, Toshinori Kojima, Yasunori Osana, Akira Funahashi, Noriko Hiroi, Yuichiro Shibata, Naoki Iwanaga, Hideki Yamada, Hiroaki Kitano, Hideharu Amano

Research output: Chapter in Book/Report/Conference proceedingConference contribution

14 Citations (Scopus)

Abstract

This paper introduces a scalable FPGA implementation of a stochastic simulation algorithm (SSA) called the Next Reaction Method. There are some hardware approaches of SSAs that obtained high-through put on reconfigurable devices such as FPGAs, but these works lacked in scalability. The design of this work can accommodate to the increasing size of target biochemical models, or to make use of increasing capacity of FPGAs. Interconnection network between arithmetic circuits and multiple simulation circuits aims to perform a data-driven multi-threading simulation. Approximately 8 times speedup was obtained compared to an execution on Xeon 2.80GHz.

Original languageEnglish
Title of host publicationProceedings - 2007 International Conference on Field Programmable Logic and Applications, FPL
Pages254-259
Number of pages6
DOIs
Publication statusPublished - 2007 Dec 1
Event2007 International Conference on Field Programmable Logic and Applications, FPL - Amsterdam, Netherlands
Duration: 2007 Aug 272007 Aug 29

Publication series

NameProceedings - 2007 International Conference on Field Programmable Logic and Applications, FPL

Other

Other2007 International Conference on Field Programmable Logic and Applications, FPL
CountryNetherlands
CityAmsterdam
Period07/8/2707/8/29

ASJC Scopus subject areas

  • Computer Science Applications
  • Electrical and Electronic Engineering

Fingerprint Dive into the research topics of 'FPGA implementation of a data-driven stochastic biochemical simulator with the next reaction method'. Together they form a unique fingerprint.

  • Cite this

    Yoshimi, M., Iwaoka, Y., Nishikawa, Y., Kojima, T., Osana, Y., Funahashi, A., Hiroi, N., Shibata, Y., Iwanaga, N., Yamada, H., Kitano, H., & Amano, H. (2007). FPGA implementation of a data-driven stochastic biochemical simulator with the next reaction method. In Proceedings - 2007 International Conference on Field Programmable Logic and Applications, FPL (pp. 254-259). [4380656] (Proceedings - 2007 International Conference on Field Programmable Logic and Applications, FPL). https://doi.org/10.1109/FPL.2007.4380656